More than 100 new gut bacteria discovered in human microbiome

Dr Sam Forster

Scientists working on the gut microbiome have discovered and isolated more than 100 completely new species of bacteria from healthy people’s intestines.

The discovery will support the development of new diagnostics and treatments for diseases such as gastrointestinal disorders, infections and immune conditions.

The study from the Hudson Institute of Medical Research and Monash University, Melbourne, the Wellcome Sanger Institute, UK, and EMBL’s European Bioinformatics Institute, has created the most comprehensive collection of human intestinal bacteria to date. This will help researchers worldwide to investigate how our microbiome keeps us healthy, and its role in disease.

Reported on Monday, 4 February (UK time), in Nature Biotechnology, the new resource will allow scientists to detect which bacteria are present in the human gut, more accurately and faster than ever before.

There are trillions of microbes in the human intestine, which form a huge ecosystem known as the gut microbiome.  These microbes are known to be important for health, and imbalances in the gut microbiome can contribute to complex conditions and diseases.

About two per cent of a person’s body weight is due to bacteria and the intestinal microbiome is a major bacterial site and an essential contributor to human health. Imbalances in our gut microbiome can contribute to diseases and complex conditions such as Inflammatory Bowel Disease, Irritable Bowel Syndrome allergies and obesity. However, as many species of gut bacteria are extremely difficult to grow in the laboratory, there is a huge gap in our knowledge of them.

New bacterial species

Standard methods to understand how the gut microbiome impacts on human health involves sequencing the DNA from mixed samples of gut bacteria to try to understand each component. However, these studies have been severely hampered by the lack of individually isolated bacteria and reference genomes from them.

In the study, researchers studied fecal samples from 20 people from the UK and Canada, and successfully grew and DNA sequenced 737 individual bacterial strains from these. Analysis of these isolates revealed 273 separate bacterial species, including 173 that had never been previously sequenced. Of these, 105 species had never even been isolated before.

“This study has led to the creation of the largest and most comprehensive public database of human health-associated intestinal bacteria. The gut microbiome plays a major role in health and disease. This important resource will fundamentally change the way researchers study the microbiome.”

Dr Samuel Forster, first author on the paper from Hudson Institute and Monash University, and Wellcome Sanger Institute

“The new culture collection and reference genomes will make it much cheaper and easier for researchers to determine which bacteria are present within communities of people and research their role in disease,” said Dr Forster.

Dr Rob Finn, an author from EMBL’s European Bioinformatics Institute, said: “For researchers trying to find out which species of bacteria are present in a person’s microbiome, the database of reference genomes from pure isolates of gut bacteria is crucial. Then if they want to test a hypothesis, for example that a particular species is enriched in a certain disease, they can get the isolate itself from the collection and physically test in the laboratory if this species seems to be important.”

Dr Trevor Lawley, senior author from the Wellcome Sanger Institute, said: “This culture collection of individual bacteria will be a game-changer for basic and translational microbiome research. By culturing the unculturable, we have created a resource that will make microbiome analysis faster, cheaper and more accurate and will allow further study of their biology and functions. Ultimately, this will lead us towards developing new diagnostics and treatments for diseases such as gastrointestinal disorders, infections and immune conditions.”

Funders: The Australian National Health and Medical Research Council (NHMRC), the Victorian Government, Wellcome, the Medical Research Council, the BBSRC, the European Molecular Biology Laboratory

Publication: Samuel C. Forster & Nitin Kumar et al. (2019) Human Gastrointestinal Bacteria Genome and Culture Collection. Nature Biotechnology. DOI: 10.1038/s41587-018-0009-7

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